Merge branch 'release/v3.0.7'

milaboratory · May 19, 2019 · 49c5599 · 49c5599
2 parents 3e0beb6 + 5717b66
commit 49c5599
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Showing 9 changed files with 51 additions and 20 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,14 @@
 
+MiXCR 3.0.7 (20 May 2019)
+========================
+
+-- Fixes clone oversplitting in assembleContigs in noizy (e.g. single-cell) data with substanial 
+   fraction of sequences with errors in `CDR3`
+-- Fixes wrong alignment-scoring-based filtering in pre-clustering procedure
+-- Fixes rare bug in export of imputed gene feature sequences
+-- minor: Better error message for mutation extraction from alignment-attached gene features
+
+
 MiXCR 3.0.6 (10 Apr 2019)
 ========================
 

diff --git a/pom.xml b/pom.xml
@@ -33,7 +33,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>3.0.6</version>
+    <version>3.0.7</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

diff --git a/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java
@@ -694,7 +694,8 @@ public List<CloneAccumulator> build() {
                     continue;
 
                 for (int j = 0; j < 3; j++) {
-                    if (accs[i].getBestScore(GeneType.VJC_REFERENCE[j]) < maxScores[j]) {
+                    if (accs[i].getBestGene(GeneType.VJC_REFERENCE[j]) != null &&
+                            accs[i].getBestScore(GeneType.VJC_REFERENCE[j]) < maxScores[j]) {
                         dropped.accept(accs[i]);
                         accs[i] = null;
                         break;

diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java
@@ -64,6 +64,7 @@
 import static io.repseq.core.GeneType.Variable;
 
 /**
+ *
  */
 public final class FullSeqAssembler {
     private static int ABSENT_PACKED_VARIANT_INFO = -1;
@@ -1518,6 +1519,6 @@ else if (right == -1)
     }
 
     private boolean inSplitRegion(int p) {
-        return splitRegion == null || splitRegion.contains(p);
+        return splitRegion != null && splitRegion.contains(p);
     }
 }
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCObject.java
@@ -464,8 +464,11 @@ public CaseSensitiveNucleotideSequence getIncompleteFeature(GeneFeature geneFeat
                 if (lHit == rHit) {
                     Alignment<NucleotideSequence> lAl = lHit.getAlignment(lLast.iTarget);
                     if (lAl.getSequence1Range().contains(rPositionInRef)) {
-                        IncompleteSequencePart part = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin,
-                                aabs(lAl.convertToSeq2Position(rPositionInRef)));
+                        int aabs = aabs(lAl.convertToSeq2Position(rPositionInRef));
+                        if (aabs < lLast.begin)
+                            return null;
+
+                        IncompleteSequencePart part = new IncompleteSequencePart(lHit, false, lLast.iTarget, lLast.begin, aabs);
                         if (part.begin == part.end)
                             leftParts.remove(leftParts.size() - 1);
                         else
@@ -481,8 +484,11 @@ public CaseSensitiveNucleotideSequence getIncompleteFeature(GeneFeature geneFeat
 
                     Alignment<NucleotideSequence> rAl = lHit.getAlignment(rLast.iTarget);
                     if (rAl.getSequence1Range().contains(lPositionInRef)) {
-                        IncompleteSequencePart part = new IncompleteSequencePart(rHit, false, rLast.iTarget,
-                                aabs(rAl.convertToSeq2Position(lPositionInRef)), rLast.end);
+                        int aabs = aabs(rAl.convertToSeq2Position(lPositionInRef));
+                        if (aabs > rLast.end)
+                            return null;
+
+                        IncompleteSequencePart part = new IncompleteSequencePart(rHit, false, rLast.iTarget, aabs, rLast.end);
                         if (part.begin == part.end)
                             rightParts.remove(0);
                         else
@@ -567,7 +573,7 @@ private static final class IncompleteSequencePart {
         final int begin, end;
 
         IncompleteSequencePart(VDJCHit hit, boolean germline, int iTarget, int begin, int end) {
-            assert begin <= end;
+            assert begin <= end : "" + begin + " - " + end;
             this.hit = hit;
             this.germline = germline;
             this.iTarget = iTarget;

diff --git a/src/main/java/com/milaboratory/mixcr/cli/Main.java b/src/main/java/com/milaboratory/mixcr/cli/Main.java
@@ -64,18 +64,20 @@ protected List<Object> handle(ParseResult parseResult) throws CommandLine.Execut
                 List<CommandLine> parsedCommands = parseResult.asCommandLineList();
                 CommandLine commandLine = parsedCommands.get(parsedCommands.size() - 1);
                 Object command = commandLine.getCommand();
-                if (command instanceof CommandSpec && ((CommandSpec) command).userObject() instanceof Runnable) {
-                    try {
+                try {
+                    if (command instanceof CommandSpec && ((CommandSpec) command).userObject() instanceof Runnable) {
                         ((Runnable) ((CommandSpec) command).userObject()).run();
                         return new ArrayList<>();
-                    } catch (ParameterException | CommandLine.ExecutionException ex) {
-                        throw ex;
-                    } catch (Exception ex) {
-                        throw new CommandLine.ExecutionException(commandLine,
-                                "Error while running command (" + command + "): " + ex, ex);
                     }
+                    return super.handle(parseResult);
+                } catch (ParameterException ex) {
+                    throw ex;
+                } catch (CommandLine.ExecutionException ex) {
+                    throw ex;
+                } catch (Exception ex) {
+                    throw new CommandLine.ExecutionException(commandLine,
+                            "Error while running command (" + command + "): " + ex, ex);
                 }
-                return super.handle(parseResult);
             }
         };
 

diff --git a/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FeatureExtractors.java
@@ -58,8 +58,6 @@ void validate(GeneFeature[] features) {
             if (features.length == 2 && !features[1].contains(features[0]))
                 throw new IllegalArgumentException(String.format("%s: Base feature %s does not contain relative feature %s",
                         command, GeneFeature.encode(features[1]), GeneFeature.encode(features[0])));
-
-            //todo bigfeature nofloating bounds
         }
 
         private String header0(String[] prefixes, GeneFeature[] features) {
@@ -122,6 +120,19 @@ void validate(GeneFeature[] features) {
                 if (feature.getGeneType() == null)
                     throw new IllegalArgumentException(String.format("%s: Gene feature %s covers several gene types " +
                             "(not possible to select corresponding alignment)", command, GeneFeature.encode(feature)));
+
+            if (features.length == 2 && features[1].isAlignmentAttached())
+                throw new IllegalArgumentException(
+                        String.format(
+                                "%s: Alignment attached base gene features not allowed (error in %s)",
+                                command, GeneFeature.encode(features[1])));
+
+            if (features.length == 1 && features[0].isAlignmentAttached())
+                throw new IllegalArgumentException(
+                        String.format(
+                                "%s: Please use %s option instead and specify base gene feature to extract mutations " +
+                                        "from alignment-attached gene feature %s",
+                                command, command + "Relative", GeneFeature.encode(features[0])));
         }
 
         @Override

diff --git a/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java b/src/main/java/com/milaboratory/mixcr/export/FieldExtractors.java
@@ -664,7 +664,7 @@ protected String extract(VDJCObject object) {
                 });
             }
 
-            descriptorsList.add(new PL_O("-chains", "Chains", "Chains", "Chains") {
+            descriptorsList.add(new PL_O("-chains", "Chains", "Chains", "chains") {
                 @Override
                 protected String extract(VDJCObject object) {
                     return object.commonChains().toString();

diff --git a/src/main/resources/parameters/full_seq_assembler_parameters.json b/src/main/resources/parameters/full_seq_assembler_parameters.json
@@ -8,7 +8,7 @@
     "alignedSequenceEdgeDelta": 3,
     "alignmentEdgeRegionSize": 7,
     "minimalNonEdgePointsFraction": 0.25,
-    "subCloningRegion": "CDR3",
+    "subCloningRegion": null,
     "trimmingParameters": {
       "averageQualityThreshold": 20.0,
       "windowSize": 8